There were no immediate reports of damage.
Beyonce Matthew, who was on the night shift at Uluru's Sails In The Desert Hotel, said some guests were jolted awake by the rumbling.
"It was only for a few minutes," she told AAP.
"The doors were shaking, but nothing fell off the bookshelves."
Nevertheless, she said the tremors came as a bit of a surprise.
The US Geological Survey said the earthquake was 77km south-southwest of Yulara and registered at a magnitude of 5.5 after it was initially reported as being slightly weaker.
"It woke a number of people up from Yulara and around the region with some light to moderate shaking," Geoscience Australia senior seismologist Jonathan Bathgate told ABC Radio.
"Some light fixtures swinging from the ceiling and some things rattling from shelves and that sort of thing - it was a bit of an early morning wake-up for quite a few people."
More than 30 reports had been lodged with the national earthquake alert centre in Canberra by early Sunday afternoon, with people describing being jolted awake but no structural damage reported.
A smaller aftershock, measured as magnitude 3.4, was recorded just after 9am but would only have been felt close to the epicentre, Dr Bathgate said.
The region has a significant seismic history, including magnitude 5.4 earthquakes recorded near Ernabella in 2012 and 2013, and a magnitude 6.1 event in the Petermann Ranges in 2016.
The overnight quake was about the same strength as the 1989 Newcastle earthquake, which caused 13 deaths and damage to an estimated 50,000 buildings.
"It's basically equivalent to what we experienced with the Newcastle earthquake … it just happens to be in quite a remote part of the country, rather than near a very populated centre," Dr Bathgate said.
While aftershocks are expected to continue, they should become less frequent and smaller over time, although a larger event cannot be completely ruled out.
Authorities will continue to monitor seismic activity in the area and assess any reports of damage.
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